Last code update: Feb 8, 202s4

User Inputs

source directory: /Users/nalbistami/Gladstone Dropbox/Noura Al Bistami/AALS Shared DropBox/GEDI Analysis/Combined Experiments/CombinedC9orf72/Class compare
output directory: /Users/nalbistami/Gladstone Dropbox/Noura Al Bistami/AALS Shared DropBox/GEDI Analysis/Combined Experiments/CombinedC9orf72/Class compare

drug: FALSE
drug kept: None
line kept: 0YX7iCTR, 6ZLDiALS, BUUiALS, 2AE8iCTR

multiple_experiments: TRUE
multiple_plates <- FALSE

compare_cellline <- FALSE
compare_class <- TRUE
compare_drug <-FALSE

reference conditions:

## 
## 
## |Experiment |Plate |CellLine | sum_live| sum_dead|
## |:----------|:-----|:--------|--------:|--------:|
## |Set26      |NA    |0YX7iCTR |    22460|      665|
## |Set26      |NA    |2AE8iCTR |    14628|      756|
## |Set26      |NA    |BUUiALS  |    12712|      775|
## |Set29      |NA    |2AE8iCTR |     5463|      350|
## |Set29      |NA    |6ZLDiALS |     7229|      351|
## |Set29      |NA    |BUUiALS  |     9774|      276|
## |Set30      |NA    |0YX7iCTR |     1409|      144|
## |Set30      |NA    |2AE8iCTR |     1670|      148|
## |Set30      |NA    |6ZLDiALS |      695|       97|
## |Set30      |NA    |BUUiALS  |     1813|      119|
## |Set32      |NA    |2AE8iCTR |     1927|      118|
## |Set32      |NA    |6ZLDiALS |      588|      269|
## |Set32      |NA    |BUUiALS  |      987|      174|
## |Set33      |NA    |0YX7iCTR |      986|       24|
## |Set33      |NA    |BUUiALS  |     8449|      339|
## |Set34      |NA    |0YX7iCTR |     1784|      112|
## |Set34      |NA    |BUUiALS  |     2177|       75|
## |Set35      |NA    |0YX7iCTR |     2274|       69|
## |Set35      |NA    |BUUiALS  |     9077|      348|
## |Set36      |NA    |2AE8iCTR |    30438|      412|
## |Set36      |NA    |6ZLDiALS |     3897|      497|
## |Set40      |NA    |0YX7iCTR |    52680|     4734|
## |Set40      |NA    |6ZLDiALS |     2945|     2454|
## |Set40      |NA    |BUUiALS  |    15073|     3233|
## |Set44      |NA    |0YX7iCTR |     7678|      957|
## |Set44      |NA    |6ZLDiALS |      869|      770|
## |Set44      |NA    |BUUiALS  |      942|      462|
## |Set45      |NA    |0YX7iCTR |    26083|     1432|
## |Set45      |NA    |6ZLDiALS |    27504|     1178|
## |Set51      |NA    |0YX7iCTR |     8098|      831|
## |Set51      |NA    |6ZLDiALS |     7716|     1271|
## |Set52      |NA    |0YX7iCTR |     2393|     1241|
## |Set52      |NA    |6ZLDiALS |      855|     2003|
## |set57      |NA    |0YX7iCTR |     9115|     1044|
## |set57      |NA    |6ZLDiALS |     4576|     2345|
## |set58      |NA    |0YX7iCTR |     2456|       84|
## |set58      |NA    |6ZLDiALS |     5988|      255|
## |set59      |NA    |0YX7iCTR |     3144|      529|
## |set59      |NA    |6ZLDiALS |     1653|      411|
## 
## 
## |Experiment |Plate |CellLine |Timepoint |Hour | sum_live| sum_dead|
## |:----------|:-----|:--------|:---------|:----|--------:|--------:|
## |Set26      |NA    |0YX7iCTR |1         |0    |     2991|       57|
## |Set26      |NA    |0YX7iCTR |2         |24   |     3209|       49|
## |Set26      |NA    |0YX7iCTR |3         |48   |     3186|       45|
## |Set26      |NA    |0YX7iCTR |4         |72   |     3081|       60|
## |Set26      |NA    |0YX7iCTR |5         |96   |     3063|       67|
## |Set26      |NA    |0YX7iCTR |6         |120  |     2439|      119|
## |Set26      |NA    |0YX7iCTR |7         |144  |     2180|      156|
## |Set26      |NA    |0YX7iCTR |8         |168  |     2311|      112|
## |Set26      |NA    |2AE8iCTR |1         |0    |     2018|       69|
## |Set26      |NA    |2AE8iCTR |2         |24   |     2366|       53|
## |Set26      |NA    |2AE8iCTR |3         |48   |     2260|       55|
## |Set26      |NA    |2AE8iCTR |4         |72   |     2040|       62|
## |Set26      |NA    |2AE8iCTR |5         |96   |     1995|       80|
## |Set26      |NA    |2AE8iCTR |6         |120  |     1405|      121|
## |Set26      |NA    |2AE8iCTR |7         |144  |     1184|      157|
## |Set26      |NA    |2AE8iCTR |8         |168  |     1360|      159|
## |Set26      |NA    |BUUiALS  |1         |0    |     1874|      121|
## |Set26      |NA    |BUUiALS  |2         |24   |     1946|       64|
## |Set26      |NA    |BUUiALS  |3         |48   |     1900|       61|
## |Set26      |NA    |BUUiALS  |4         |72   |     1738|       60|
## |Set26      |NA    |BUUiALS  |5         |96   |     1736|       55|
## |Set26      |NA    |BUUiALS  |6         |120  |     1242|      129|
## |Set26      |NA    |BUUiALS  |7         |144  |     1092|      167|
## |Set26      |NA    |BUUiALS  |8         |168  |     1184|      118|
## |Set29      |NA    |2AE8iCTR |1         |0    |     1201|       47|
## |Set29      |NA    |2AE8iCTR |2         |24   |      931|       37|
## |Set29      |NA    |2AE8iCTR |3         |48   |     1091|       35|
## |Set29      |NA    |2AE8iCTR |6         |120  |      678|       68|
## |Set29      |NA    |2AE8iCTR |7         |144  |      780|       86|
## |Set29      |NA    |2AE8iCTR |8         |168  |      782|       77|
## |Set29      |NA    |6ZLDiALS |1         |0    |     1351|       41|
## |Set29      |NA    |6ZLDiALS |2         |24   |     1256|       41|
## |Set29      |NA    |6ZLDiALS |3         |48   |     1358|       47|
## |Set29      |NA    |6ZLDiALS |6         |120  |      941|       84|
## |Set29      |NA    |6ZLDiALS |7         |144  |     1143|       66|
## |Set29      |NA    |6ZLDiALS |8         |168  |     1180|       72|
## |Set29      |NA    |BUUiALS  |1         |0    |     1806|       42|
## |Set29      |NA    |BUUiALS  |2         |24   |     1540|       35|
## |Set29      |NA    |BUUiALS  |3         |48   |     1696|       37|
## |Set29      |NA    |BUUiALS  |6         |120  |     1498|       52|
## |Set29      |NA    |BUUiALS  |7         |144  |     1595|       46|
## |Set29      |NA    |BUUiALS  |8         |168  |     1639|       64|
## |Set30      |NA    |0YX7iCTR |1         |0    |      111|       18|
## |Set30      |NA    |0YX7iCTR |2         |24   |      122|       17|
## |Set30      |NA    |0YX7iCTR |3         |48   |      139|       15|
## |Set30      |NA    |0YX7iCTR |4         |72   |      151|       15|
## |Set30      |NA    |0YX7iCTR |5         |96   |      149|       14|
## |Set30      |NA    |0YX7iCTR |6         |120  |      188|       17|
## |Set30      |NA    |0YX7iCTR |7         |144  |      188|       11|
## |Set30      |NA    |0YX7iCTR |8         |168  |      185|       21|
## |Set30      |NA    |0YX7iCTR |9         |192  |      176|       16|
## |Set30      |NA    |2AE8iCTR |1         |0    |       62|       20|
## |Set30      |NA    |2AE8iCTR |2         |24   |      106|       32|
## |Set30      |NA    |2AE8iCTR |3         |48   |      109|       24|
## |Set30      |NA    |2AE8iCTR |4         |72   |      181|       21|
## |Set30      |NA    |2AE8iCTR |5         |96   |      215|       15|
## |Set30      |NA    |2AE8iCTR |6         |120  |      288|       14|
## |Set30      |NA    |2AE8iCTR |7         |144  |      236|        4|
## |Set30      |NA    |2AE8iCTR |8         |168  |      252|        5|
## |Set30      |NA    |2AE8iCTR |9         |192  |      221|       13|
## |Set30      |NA    |6ZLDiALS |1         |0    |       32|        9|
## |Set30      |NA    |6ZLDiALS |2         |24   |       48|       13|
## |Set30      |NA    |6ZLDiALS |3         |48   |       63|       16|
## |Set30      |NA    |6ZLDiALS |4         |72   |       87|        8|
## |Set30      |NA    |6ZLDiALS |5         |96   |       83|        5|
## |Set30      |NA    |6ZLDiALS |6         |120  |       89|        9|
## |Set30      |NA    |6ZLDiALS |7         |144  |       91|       12|
## |Set30      |NA    |6ZLDiALS |8         |168  |      105|        8|
## |Set30      |NA    |6ZLDiALS |9         |192  |       97|       17|
## |Set30      |NA    |BUUiALS  |1         |0    |      120|        7|
## |Set30      |NA    |BUUiALS  |2         |24   |      124|       14|
## |Set30      |NA    |BUUiALS  |3         |48   |      159|       15|
## |Set30      |NA    |BUUiALS  |4         |72   |      188|       10|
## |Set30      |NA    |BUUiALS  |5         |96   |      203|       14|
## |Set30      |NA    |BUUiALS  |6         |120  |      238|       12|
## |Set30      |NA    |BUUiALS  |7         |144  |      258|       21|
## |Set30      |NA    |BUUiALS  |8         |168  |      269|       14|
## |Set30      |NA    |BUUiALS  |9         |192  |      254|       12|
## |Set32      |NA    |2AE8iCTR |1         |0    |      157|       10|
## |Set32      |NA    |2AE8iCTR |2         |24   |      187|       13|
## |Set32      |NA    |2AE8iCTR |3         |48   |      238|       16|
## |Set32      |NA    |2AE8iCTR |4         |72   |      249|        7|
## |Set32      |NA    |2AE8iCTR |5         |96   |      287|       15|
## |Set32      |NA    |2AE8iCTR |6         |120  |      269|       17|
## |Set32      |NA    |2AE8iCTR |7         |144  |      243|       23|
## |Set32      |NA    |2AE8iCTR |8         |168  |      297|       17|
## |Set32      |NA    |6ZLDiALS |1         |0    |       58|       26|
## |Set32      |NA    |6ZLDiALS |2         |24   |       47|       33|
## |Set32      |NA    |6ZLDiALS |3         |48   |       75|       30|
## |Set32      |NA    |6ZLDiALS |4         |72   |       80|       35|
## |Set32      |NA    |6ZLDiALS |5         |96   |       81|       43|
## |Set32      |NA    |6ZLDiALS |6         |120  |       78|       34|
## |Set32      |NA    |6ZLDiALS |7         |144  |       82|       34|
## |Set32      |NA    |6ZLDiALS |8         |168  |       87|       34|
## |Set32      |NA    |BUUiALS  |1         |0    |       91|       13|
## |Set32      |NA    |BUUiALS  |2         |24   |      122|       16|
## |Set32      |NA    |BUUiALS  |3         |48   |      142|       17|
## |Set32      |NA    |BUUiALS  |4         |72   |      154|       17|
## |Set32      |NA    |BUUiALS  |5         |96   |      137|       33|
## |Set32      |NA    |BUUiALS  |6         |120  |       74|       13|
## |Set32      |NA    |BUUiALS  |7         |144  |      125|       30|
## |Set32      |NA    |BUUiALS  |8         |168  |      142|       35|
## |Set33      |NA    |0YX7iCTR |1         |0    |      185|        3|
## |Set33      |NA    |0YX7iCTR |2         |24   |      203|        4|
## |Set33      |NA    |0YX7iCTR |5         |96   |      204|        5|
## |Set33      |NA    |0YX7iCTR |6         |120  |      194|        7|
## |Set33      |NA    |0YX7iCTR |8         |168  |      200|        5|
## |Set33      |NA    |BUUiALS  |1         |0    |     1934|       94|
## |Set33      |NA    |BUUiALS  |2         |24   |     1918|       76|
## |Set33      |NA    |BUUiALS  |5         |96   |     1999|       65|
## |Set33      |NA    |BUUiALS  |6         |120  |     1766|       55|
## |Set33      |NA    |BUUiALS  |8         |168  |      832|       49|
## |Set34      |NA    |0YX7iCTR |1         |0    |      415|       23|
## |Set34      |NA    |0YX7iCTR |6         |120  |      453|       22|
## |Set34      |NA    |0YX7iCTR |7         |144  |      460|       33|
## |Set34      |NA    |0YX7iCTR |8         |168  |      456|       34|
## |Set34      |NA    |BUUiALS  |1         |0    |      497|       26|
## |Set34      |NA    |BUUiALS  |6         |120  |      563|       15|
## |Set34      |NA    |BUUiALS  |7         |144  |      562|       13|
## |Set34      |NA    |BUUiALS  |8         |168  |      555|       21|
## |Set35      |NA    |0YX7iCTR |1         |0    |      446|        7|
## |Set35      |NA    |0YX7iCTR |2         |24   |      485|        7|
## |Set35      |NA    |0YX7iCTR |3         |48   |      437|       10|
## |Set35      |NA    |0YX7iCTR |4         |72   |      357|       11|
## |Set35      |NA    |0YX7iCTR |5         |96   |      296|       13|
## |Set35      |NA    |0YX7iCTR |6         |120  |      253|       21|
## |Set35      |NA    |BUUiALS  |1         |0    |     1283|       23|
## |Set35      |NA    |BUUiALS  |2         |24   |     1421|       33|
## |Set35      |NA    |BUUiALS  |3         |48   |     1683|       62|
## |Set35      |NA    |BUUiALS  |4         |72   |     1619|       70|
## |Set35      |NA    |BUUiALS  |5         |96   |     1565|       82|
## |Set35      |NA    |BUUiALS  |6         |120  |     1506|       78|
## |Set36      |NA    |2AE8iCTR |1         |0    |     3746|       29|
## |Set36      |NA    |2AE8iCTR |2         |24   |     4034|       29|
## |Set36      |NA    |2AE8iCTR |3         |48   |     3723|       37|
## |Set36      |NA    |2AE8iCTR |4         |72   |     3863|       59|
## |Set36      |NA    |2AE8iCTR |5         |96   |     4025|       74|
## |Set36      |NA    |2AE8iCTR |6         |120  |     3961|       77|
## |Set36      |NA    |2AE8iCTR |7         |144  |     3573|       52|
## |Set36      |NA    |2AE8iCTR |8         |168  |     3513|       55|
## |Set36      |NA    |6ZLDiALS |1         |0    |      367|       21|
## |Set36      |NA    |6ZLDiALS |2         |24   |      470|       51|
## |Set36      |NA    |6ZLDiALS |3         |48   |      516|       35|
## |Set36      |NA    |6ZLDiALS |4         |72   |      557|       57|
## |Set36      |NA    |6ZLDiALS |5         |96   |      554|       87|
## |Set36      |NA    |6ZLDiALS |6         |120  |      527|       88|
## |Set36      |NA    |6ZLDiALS |7         |144  |      506|       78|
## |Set36      |NA    |6ZLDiALS |8         |168  |      400|       80|
## |Set40      |NA    |0YX7iCTR |1         |0    |     4891|      235|
## |Set40      |NA    |0YX7iCTR |2         |24   |     5540|      413|
## |Set40      |NA    |0YX7iCTR |3         |48   |     5770|      441|
## |Set40      |NA    |0YX7iCTR |4         |72   |     6004|      474|
## |Set40      |NA    |0YX7iCTR |5         |96   |     5927|      493|
## |Set40      |NA    |0YX7iCTR |6         |120  |     5993|      594|
## |Set40      |NA    |0YX7iCTR |7         |144  |     6053|      600|
## |Set40      |NA    |0YX7iCTR |8         |168  |     6200|      699|
## |Set40      |NA    |0YX7iCTR |9         |192  |     6302|      785|
## |Set40      |NA    |6ZLDiALS |1         |0    |      420|      330|
## |Set40      |NA    |6ZLDiALS |2         |24   |      323|      349|
## |Set40      |NA    |6ZLDiALS |3         |48   |      299|      332|
## |Set40      |NA    |6ZLDiALS |4         |72   |      321|      242|
## |Set40      |NA    |6ZLDiALS |5         |96   |      290|      253|
## |Set40      |NA    |6ZLDiALS |6         |120  |      294|      206|
## |Set40      |NA    |6ZLDiALS |7         |144  |      335|      235|
## |Set40      |NA    |6ZLDiALS |8         |168  |      335|      250|
## |Set40      |NA    |6ZLDiALS |9         |192  |      328|      257|
## |Set40      |NA    |BUUiALS  |1         |0    |     2596|      485|
## |Set40      |NA    |BUUiALS  |2         |24   |     2133|      491|
## |Set40      |NA    |BUUiALS  |3         |48   |     1892|      377|
## |Set40      |NA    |BUUiALS  |4         |72   |     1777|      324|
## |Set40      |NA    |BUUiALS  |5         |96   |     1492|      305|
## |Set40      |NA    |BUUiALS  |6         |120  |     1394|      328|
## |Set40      |NA    |BUUiALS  |7         |144  |     1256|      314|
## |Set40      |NA    |BUUiALS  |8         |168  |     1286|      311|
## |Set40      |NA    |BUUiALS  |9         |192  |     1247|      298|
## |Set44      |NA    |0YX7iCTR |1         |0    |      800|      291|
## |Set44      |NA    |0YX7iCTR |2         |24   |     1836|      117|
## |Set44      |NA    |0YX7iCTR |3         |48   |     1785|       88|
## |Set44      |NA    |0YX7iCTR |4         |72   |     1721|      116|
## |Set44      |NA    |0YX7iCTR |5         |96   |      803|      192|
## |Set44      |NA    |0YX7iCTR |8         |168  |      733|      153|
## |Set44      |NA    |6ZLDiALS |1         |0    |      125|      272|
## |Set44      |NA    |6ZLDiALS |2         |24   |      239|      142|
## |Set44      |NA    |6ZLDiALS |3         |48   |      221|       76|
## |Set44      |NA    |6ZLDiALS |4         |72   |      151|       84|
## |Set44      |NA    |6ZLDiALS |5         |96   |       82|      102|
## |Set44      |NA    |6ZLDiALS |8         |168  |       51|       94|
## |Set44      |NA    |BUUiALS  |1         |0    |      123|      173|
## |Set44      |NA    |BUUiALS  |2         |24   |      272|       79|
## |Set44      |NA    |BUUiALS  |3         |48   |      260|       73|
## |Set44      |NA    |BUUiALS  |4         |72   |      182|       44|
## |Set44      |NA    |BUUiALS  |5         |96   |       76|       45|
## |Set44      |NA    |BUUiALS  |8         |168  |       29|       48|
## |Set45      |NA    |0YX7iCTR |1         |0    |     4183|      173|
## |Set45      |NA    |0YX7iCTR |2         |24   |     3602|       87|
## |Set45      |NA    |0YX7iCTR |3         |48   |     3324|      216|
## |Set45      |NA    |0YX7iCTR |4         |72   |     2512|      219|
## |Set45      |NA    |0YX7iCTR |5         |96   |     2619|      118|
## |Set45      |NA    |0YX7iCTR |6         |120  |     2444|      107|
## |Set45      |NA    |0YX7iCTR |7         |144  |     1878|      166|
## |Set45      |NA    |0YX7iCTR |8         |168  |     1588|      102|
## |Set45      |NA    |0YX7iCTR |9         |192  |     2050|       89|
## |Set45      |NA    |0YX7iCTR |10        |216  |     1883|      155|
## |Set45      |NA    |6ZLDiALS |1         |0    |     3588|       69|
## |Set45      |NA    |6ZLDiALS |2         |24   |     3383|       91|
## |Set45      |NA    |6ZLDiALS |3         |48   |     3301|      140|
## |Set45      |NA    |6ZLDiALS |4         |72   |     2818|       95|
## |Set45      |NA    |6ZLDiALS |5         |96   |     3223|      152|
## |Set45      |NA    |6ZLDiALS |6         |120  |     3037|      112|
## |Set45      |NA    |6ZLDiALS |7         |144  |     2034|      175|
## |Set45      |NA    |6ZLDiALS |8         |168  |     1773|       75|
## |Set45      |NA    |6ZLDiALS |9         |192  |     2256|      137|
## |Set45      |NA    |6ZLDiALS |10        |216  |     2091|      132|
## |Set51      |NA    |0YX7iCTR |1         |0    |      880|       45|
## |Set51      |NA    |0YX7iCTR |2         |24   |      976|       46|
## |Set51      |NA    |0YX7iCTR |3         |48   |      746|       43|
## |Set51      |NA    |0YX7iCTR |4         |72   |     1058|       63|
## |Set51      |NA    |0YX7iCTR |5         |96   |     1080|       70|
## |Set51      |NA    |0YX7iCTR |6         |120  |      744|      105|
## |Set51      |NA    |0YX7iCTR |7         |144  |      926|       93|
## |Set51      |NA    |0YX7iCTR |8         |168  |      814|      163|
## |Set51      |NA    |0YX7iCTR |9         |192  |      874|      203|
## |Set51      |NA    |6ZLDiALS |1         |0    |      524|      147|
## |Set51      |NA    |6ZLDiALS |2         |24   |      737|      123|
## |Set51      |NA    |6ZLDiALS |3         |48   |      776|      122|
## |Set51      |NA    |6ZLDiALS |4         |72   |      972|      114|
## |Set51      |NA    |6ZLDiALS |5         |96   |     1047|      109|
## |Set51      |NA    |6ZLDiALS |6         |120  |      794|      108|
## |Set51      |NA    |6ZLDiALS |7         |144  |     1049|      123|
## |Set51      |NA    |6ZLDiALS |8         |168  |      833|      178|
## |Set51      |NA    |6ZLDiALS |9         |192  |      984|      247|
## |Set52      |NA    |0YX7iCTR |1         |0    |      323|       82|
## |Set52      |NA    |0YX7iCTR |2         |24   |      490|      191|
## |Set52      |NA    |0YX7iCTR |3         |48   |      614|      215|
## |Set52      |NA    |0YX7iCTR |4         |72   |      405|      388|
## |Set52      |NA    |0YX7iCTR |5         |96   |      561|      365|
## |Set52      |NA    |6ZLDiALS |1         |0    |      152|      175|
## |Set52      |NA    |6ZLDiALS |2         |24   |      215|      367|
## |Set52      |NA    |6ZLDiALS |3         |48   |      257|      496|
## |Set52      |NA    |6ZLDiALS |4         |72   |      105|      549|
## |Set52      |NA    |6ZLDiALS |5         |96   |      126|      416|
## |set57      |NA    |0YX7iCTR |1         |0    |      731|       68|
## |set57      |NA    |0YX7iCTR |2         |24   |      990|       55|
## |set57      |NA    |0YX7iCTR |3         |48   |      635|       67|
## |set57      |NA    |0YX7iCTR |4         |72   |      877|       47|
## |set57      |NA    |0YX7iCTR |5         |96   |      929|       49|
## |set57      |NA    |0YX7iCTR |6         |120  |      377|      104|
## |set57      |NA    |0YX7iCTR |7         |144  |      795|       74|
## |set57      |NA    |0YX7iCTR |8         |168  |      571|      106|
## |set57      |NA    |0YX7iCTR |9         |192  |      912|       98|
## |set57      |NA    |0YX7iCTR |10        |216  |      550|      193|
## |set57      |NA    |0YX7iCTR |11        |240  |      892|       85|
## |set57      |NA    |0YX7iCTR |12        |264  |      856|       98|
## |set57      |NA    |6ZLDiALS |1         |0    |      321|      247|
## |set57      |NA    |6ZLDiALS |2         |24   |      490|      199|
## |set57      |NA    |6ZLDiALS |3         |48   |      586|      277|
## |set57      |NA    |6ZLDiALS |4         |72   |      668|      244|
## |set57      |NA    |6ZLDiALS |5         |96   |      790|      229|
## |set57      |NA    |6ZLDiALS |6         |120  |      558|      270|
## |set57      |NA    |6ZLDiALS |7         |144  |      539|      246|
## |set57      |NA    |6ZLDiALS |8         |168  |      229|      191|
## |set57      |NA    |6ZLDiALS |9         |192  |      241|      161|
## |set57      |NA    |6ZLDiALS |10        |216  |       82|      119|
## |set57      |NA    |6ZLDiALS |11        |240  |       62|       94|
## |set57      |NA    |6ZLDiALS |12        |264  |       10|       68|
## |set58      |NA    |0YX7iCTR |1         |0    |      709|       24|
## |set58      |NA    |0YX7iCTR |3         |48   |      340|        4|
## |set58      |NA    |0YX7iCTR |4         |72   |      232|        5|
## |set58      |NA    |0YX7iCTR |5         |96   |      177|        6|
## |set58      |NA    |0YX7iCTR |6         |120  |      140|        4|
## |set58      |NA    |0YX7iCTR |8         |168  |      187|        9|
## |set58      |NA    |0YX7iCTR |9         |192  |      161|        7|
## |set58      |NA    |0YX7iCTR |11        |240  |      274|       12|
## |set58      |NA    |0YX7iCTR |12        |264  |      236|       13|
## |set58      |NA    |6ZLDiALS |1         |0    |      773|       24|
## |set58      |NA    |6ZLDiALS |3         |48   |      726|       39|
## |set58      |NA    |6ZLDiALS |4         |72   |      628|       21|
## |set58      |NA    |6ZLDiALS |5         |96   |      617|       25|
## |set58      |NA    |6ZLDiALS |6         |120  |      573|       23|
## |set58      |NA    |6ZLDiALS |8         |168  |      637|       22|
## |set58      |NA    |6ZLDiALS |9         |192  |      600|       24|
## |set58      |NA    |6ZLDiALS |11        |240  |      742|       41|
## |set58      |NA    |6ZLDiALS |12        |264  |      692|       36|
## |set59      |NA    |0YX7iCTR |1         |0    |      167|       51|
## |set59      |NA    |0YX7iCTR |2         |24   |      223|       57|
## |set59      |NA    |0YX7iCTR |3         |48   |      229|       37|
## |set59      |NA    |0YX7iCTR |4         |72   |      271|       43|
## |set59      |NA    |0YX7iCTR |5         |96   |      264|       47|
## |set59      |NA    |0YX7iCTR |6         |120  |      250|       53|
## |set59      |NA    |0YX7iCTR |7         |144  |      272|       31|
## |set59      |NA    |0YX7iCTR |8         |168  |      280|       42|
## |set59      |NA    |0YX7iCTR |9         |192  |      302|       41|
## |set59      |NA    |0YX7iCTR |10        |216  |      278|       40|
## |set59      |NA    |0YX7iCTR |11        |240  |      324|       47|
## |set59      |NA    |0YX7iCTR |12        |264  |      284|       40|
## |set59      |NA    |6ZLDiALS |1         |0    |       95|       50|
## |set59      |NA    |6ZLDiALS |2         |24   |       78|       63|
## |set59      |NA    |6ZLDiALS |3         |48   |       83|       35|
## |set59      |NA    |6ZLDiALS |4         |72   |      116|       19|
## |set59      |NA    |6ZLDiALS |5         |96   |      122|       24|
## |set59      |NA    |6ZLDiALS |6         |120  |      166|       29|
## |set59      |NA    |6ZLDiALS |7         |144  |      157|       28|
## |set59      |NA    |6ZLDiALS |8         |168  |      175|       44|
## |set59      |NA    |6ZLDiALS |9         |192  |      170|       36|
## |set59      |NA    |6ZLDiALS |10        |216  |      183|       30|
## |set59      |NA    |6ZLDiALS |11        |240  |      182|       30|
## |set59      |NA    |6ZLDiALS |12        |264  |      126|       23|
## 
## 
## |Experiment |Plate |Class |Timepoint | sum_live| sum_dead|
## |:----------|:-----|:-----|:---------|--------:|--------:|
## |Set26      |NA    |0     |1         |     5009|      126|
## |Set26      |NA    |0     |2         |     5575|      102|
## |Set26      |NA    |0     |3         |     5446|      100|
## |Set26      |NA    |0     |4         |     5121|      122|
## |Set26      |NA    |0     |5         |     5058|      147|
## |Set26      |NA    |0     |6         |     3844|      240|
## |Set26      |NA    |0     |7         |     3364|      313|
## |Set26      |NA    |0     |8         |     3671|      271|
## |Set26      |NA    |1     |1         |     1874|      121|
## |Set26      |NA    |1     |2         |     1946|       64|
## |Set26      |NA    |1     |3         |     1900|       61|
## |Set26      |NA    |1     |4         |     1738|       60|
## |Set26      |NA    |1     |5         |     1736|       55|
## |Set26      |NA    |1     |6         |     1242|      129|
## |Set26      |NA    |1     |7         |     1092|      167|
## |Set26      |NA    |1     |8         |     1184|      118|
## |Set29      |NA    |0     |1         |     1201|       47|
## |Set29      |NA    |0     |2         |      931|       37|
## |Set29      |NA    |0     |3         |     1091|       35|
## |Set29      |NA    |0     |6         |      678|       68|
## |Set29      |NA    |0     |7         |      780|       86|
## |Set29      |NA    |0     |8         |      782|       77|
## |Set29      |NA    |1     |1         |     3157|       83|
## |Set29      |NA    |1     |2         |     2796|       76|
## |Set29      |NA    |1     |3         |     3054|       84|
## |Set29      |NA    |1     |6         |     2439|      136|
## |Set29      |NA    |1     |7         |     2738|      112|
## |Set29      |NA    |1     |8         |     2819|      136|
## |Set30      |NA    |0     |1         |      173|       38|
## |Set30      |NA    |0     |2         |      228|       49|
## |Set30      |NA    |0     |3         |      248|       39|
## |Set30      |NA    |0     |4         |      332|       36|
## |Set30      |NA    |0     |5         |      364|       29|
## |Set30      |NA    |0     |6         |      476|       31|
## |Set30      |NA    |0     |7         |      424|       15|
## |Set30      |NA    |0     |8         |      437|       26|
## |Set30      |NA    |0     |9         |      397|       29|
## |Set30      |NA    |1     |1         |      152|       16|
## |Set30      |NA    |1     |2         |      172|       27|
## |Set30      |NA    |1     |3         |      222|       31|
## |Set30      |NA    |1     |4         |      275|       18|
## |Set30      |NA    |1     |5         |      286|       19|
## |Set30      |NA    |1     |6         |      327|       21|
## |Set30      |NA    |1     |7         |      349|       33|
## |Set30      |NA    |1     |8         |      374|       22|
## |Set30      |NA    |1     |9         |      351|       29|
## |Set32      |NA    |0     |1         |      157|       10|
## |Set32      |NA    |0     |2         |      187|       13|
## |Set32      |NA    |0     |3         |      238|       16|
## |Set32      |NA    |0     |4         |      249|        7|
## |Set32      |NA    |0     |5         |      287|       15|
## |Set32      |NA    |0     |6         |      269|       17|
## |Set32      |NA    |0     |7         |      243|       23|
## |Set32      |NA    |0     |8         |      297|       17|
## |Set32      |NA    |1     |1         |      149|       39|
## |Set32      |NA    |1     |2         |      169|       49|
## |Set32      |NA    |1     |3         |      217|       47|
## |Set32      |NA    |1     |4         |      234|       52|
## |Set32      |NA    |1     |5         |      218|       76|
## |Set32      |NA    |1     |6         |      152|       47|
## |Set32      |NA    |1     |7         |      207|       64|
## |Set32      |NA    |1     |8         |      229|       69|
## |Set33      |NA    |0     |1         |      185|        3|
## |Set33      |NA    |0     |2         |      203|        4|
## |Set33      |NA    |0     |5         |      204|        5|
## |Set33      |NA    |0     |6         |      194|        7|
## |Set33      |NA    |0     |8         |      200|        5|
## |Set33      |NA    |1     |1         |     1934|       94|
## |Set33      |NA    |1     |2         |     1918|       76|
## |Set33      |NA    |1     |5         |     1999|       65|
## |Set33      |NA    |1     |6         |     1766|       55|
## |Set33      |NA    |1     |8         |      832|       49|
## |Set34      |NA    |0     |1         |      415|       23|
## |Set34      |NA    |0     |6         |      453|       22|
## |Set34      |NA    |0     |7         |      460|       33|
## |Set34      |NA    |0     |8         |      456|       34|
## |Set34      |NA    |1     |1         |      497|       26|
## |Set34      |NA    |1     |6         |      563|       15|
## |Set34      |NA    |1     |7         |      562|       13|
## |Set34      |NA    |1     |8         |      555|       21|
## |Set35      |NA    |0     |1         |      446|        7|
## |Set35      |NA    |0     |2         |      485|        7|
## |Set35      |NA    |0     |3         |      437|       10|
## |Set35      |NA    |0     |4         |      357|       11|
## |Set35      |NA    |0     |5         |      296|       13|
## |Set35      |NA    |0     |6         |      253|       21|
## |Set35      |NA    |1     |1         |     1283|       23|
## |Set35      |NA    |1     |2         |     1421|       33|
## |Set35      |NA    |1     |3         |     1683|       62|
## |Set35      |NA    |1     |4         |     1619|       70|
## |Set35      |NA    |1     |5         |     1565|       82|
## |Set35      |NA    |1     |6         |     1506|       78|
## |Set36      |NA    |0     |1         |     3746|       29|
## |Set36      |NA    |0     |2         |     4034|       29|
## |Set36      |NA    |0     |3         |     3723|       37|
## |Set36      |NA    |0     |4         |     3863|       59|
## |Set36      |NA    |0     |5         |     4025|       74|
## |Set36      |NA    |0     |6         |     3961|       77|
## |Set36      |NA    |0     |7         |     3573|       52|
## |Set36      |NA    |0     |8         |     3513|       55|
## |Set36      |NA    |1     |1         |      367|       21|
## |Set36      |NA    |1     |2         |      470|       51|
## |Set36      |NA    |1     |3         |      516|       35|
## |Set36      |NA    |1     |4         |      557|       57|
## |Set36      |NA    |1     |5         |      554|       87|
## |Set36      |NA    |1     |6         |      527|       88|
## |Set36      |NA    |1     |7         |      506|       78|
## |Set36      |NA    |1     |8         |      400|       80|
## |Set40      |NA    |0     |1         |     4891|      235|
## |Set40      |NA    |0     |2         |     5540|      413|
## |Set40      |NA    |0     |3         |     5770|      441|
## |Set40      |NA    |0     |4         |     6004|      474|
## |Set40      |NA    |0     |5         |     5927|      493|
## |Set40      |NA    |0     |6         |     5993|      594|
## |Set40      |NA    |0     |7         |     6053|      600|
## |Set40      |NA    |0     |8         |     6200|      699|
## |Set40      |NA    |0     |9         |     6302|      785|
## |Set40      |NA    |1     |1         |     3016|      815|
## |Set40      |NA    |1     |2         |     2456|      840|
## |Set40      |NA    |1     |3         |     2191|      709|
## |Set40      |NA    |1     |4         |     2098|      566|
## |Set40      |NA    |1     |5         |     1782|      558|
## |Set40      |NA    |1     |6         |     1688|      534|
## |Set40      |NA    |1     |7         |     1591|      549|
## |Set40      |NA    |1     |8         |     1621|      561|
## |Set40      |NA    |1     |9         |     1575|      555|
## |Set44      |NA    |0     |1         |      800|      291|
## |Set44      |NA    |0     |2         |     1836|      117|
## |Set44      |NA    |0     |3         |     1785|       88|
## |Set44      |NA    |0     |4         |     1721|      116|
## |Set44      |NA    |0     |5         |      803|      192|
## |Set44      |NA    |0     |8         |      733|      153|
## |Set44      |NA    |1     |1         |      248|      445|
## |Set44      |NA    |1     |2         |      511|      221|
## |Set44      |NA    |1     |3         |      481|      149|
## |Set44      |NA    |1     |4         |      333|      128|
## |Set44      |NA    |1     |5         |      158|      147|
## |Set44      |NA    |1     |8         |       80|      142|
## |Set45      |NA    |0     |1         |     4183|      173|
## |Set45      |NA    |0     |2         |     3602|       87|
## |Set45      |NA    |0     |3         |     3324|      216|
## |Set45      |NA    |0     |4         |     2512|      219|
## |Set45      |NA    |0     |5         |     2619|      118|
## |Set45      |NA    |0     |6         |     2444|      107|
## |Set45      |NA    |0     |7         |     1878|      166|
## |Set45      |NA    |0     |8         |     1588|      102|
## |Set45      |NA    |0     |9         |     2050|       89|
## |Set45      |NA    |0     |10        |     1883|      155|
## |Set45      |NA    |1     |1         |     3588|       69|
## |Set45      |NA    |1     |2         |     3383|       91|
## |Set45      |NA    |1     |3         |     3301|      140|
## |Set45      |NA    |1     |4         |     2818|       95|
## |Set45      |NA    |1     |5         |     3223|      152|
## |Set45      |NA    |1     |6         |     3037|      112|
## |Set45      |NA    |1     |7         |     2034|      175|
## |Set45      |NA    |1     |8         |     1773|       75|
## |Set45      |NA    |1     |9         |     2256|      137|
## |Set45      |NA    |1     |10        |     2091|      132|
## |Set51      |NA    |0     |1         |      880|       45|
## |Set51      |NA    |0     |2         |      976|       46|
## |Set51      |NA    |0     |3         |      746|       43|
## |Set51      |NA    |0     |4         |     1058|       63|
## |Set51      |NA    |0     |5         |     1080|       70|
## |Set51      |NA    |0     |6         |      744|      105|
## |Set51      |NA    |0     |7         |      926|       93|
## |Set51      |NA    |0     |8         |      814|      163|
## |Set51      |NA    |0     |9         |      874|      203|
## |Set51      |NA    |1     |1         |      524|      147|
## |Set51      |NA    |1     |2         |      737|      123|
## |Set51      |NA    |1     |3         |      776|      122|
## |Set51      |NA    |1     |4         |      972|      114|
## |Set51      |NA    |1     |5         |     1047|      109|
## |Set51      |NA    |1     |6         |      794|      108|
## |Set51      |NA    |1     |7         |     1049|      123|
## |Set51      |NA    |1     |8         |      833|      178|
## |Set51      |NA    |1     |9         |      984|      247|
## |Set52      |NA    |0     |1         |      323|       82|
## |Set52      |NA    |0     |2         |      490|      191|
## |Set52      |NA    |0     |3         |      614|      215|
## |Set52      |NA    |0     |4         |      405|      388|
## |Set52      |NA    |0     |5         |      561|      365|
## |Set52      |NA    |1     |1         |      152|      175|
## |Set52      |NA    |1     |2         |      215|      367|
## |Set52      |NA    |1     |3         |      257|      496|
## |Set52      |NA    |1     |4         |      105|      549|
## |Set52      |NA    |1     |5         |      126|      416|
## |set57      |NA    |0     |1         |      731|       68|
## |set57      |NA    |0     |2         |      990|       55|
## |set57      |NA    |0     |3         |      635|       67|
## |set57      |NA    |0     |4         |      877|       47|
## |set57      |NA    |0     |5         |      929|       49|
## |set57      |NA    |0     |6         |      377|      104|
## |set57      |NA    |0     |7         |      795|       74|
## |set57      |NA    |0     |8         |      571|      106|
## |set57      |NA    |0     |9         |      912|       98|
## |set57      |NA    |0     |10        |      550|      193|
## |set57      |NA    |0     |11        |      892|       85|
## |set57      |NA    |0     |12        |      856|       98|
## |set57      |NA    |1     |1         |      321|      247|
## |set57      |NA    |1     |2         |      490|      199|
## |set57      |NA    |1     |3         |      586|      277|
## |set57      |NA    |1     |4         |      668|      244|
## |set57      |NA    |1     |5         |      790|      229|
## |set57      |NA    |1     |6         |      558|      270|
## |set57      |NA    |1     |7         |      539|      246|
## |set57      |NA    |1     |8         |      229|      191|
## |set57      |NA    |1     |9         |      241|      161|
## |set57      |NA    |1     |10        |       82|      119|
## |set57      |NA    |1     |11        |       62|       94|
## |set57      |NA    |1     |12        |       10|       68|
## |set58      |NA    |0     |1         |      709|       24|
## |set58      |NA    |0     |3         |      340|        4|
## |set58      |NA    |0     |4         |      232|        5|
## |set58      |NA    |0     |5         |      177|        6|
## |set58      |NA    |0     |6         |      140|        4|
## |set58      |NA    |0     |8         |      187|        9|
## |set58      |NA    |0     |9         |      161|        7|
## |set58      |NA    |0     |11        |      274|       12|
## |set58      |NA    |0     |12        |      236|       13|
## |set58      |NA    |1     |1         |      773|       24|
## |set58      |NA    |1     |3         |      726|       39|
## |set58      |NA    |1     |4         |      628|       21|
## |set58      |NA    |1     |5         |      617|       25|
## |set58      |NA    |1     |6         |      573|       23|
## |set58      |NA    |1     |8         |      637|       22|
## |set58      |NA    |1     |9         |      600|       24|
## |set58      |NA    |1     |11        |      742|       41|
## |set58      |NA    |1     |12        |      692|       36|
## |set59      |NA    |0     |1         |      167|       51|
## |set59      |NA    |0     |2         |      223|       57|
## |set59      |NA    |0     |3         |      229|       37|
## |set59      |NA    |0     |4         |      271|       43|
## |set59      |NA    |0     |5         |      264|       47|
## |set59      |NA    |0     |6         |      250|       53|
## |set59      |NA    |0     |7         |      272|       31|
## |set59      |NA    |0     |8         |      280|       42|
## |set59      |NA    |0     |9         |      302|       41|
## |set59      |NA    |0     |10        |      278|       40|
## |set59      |NA    |0     |11        |      324|       47|
## |set59      |NA    |0     |12        |      284|       40|
## |set59      |NA    |1     |1         |       95|       50|
## |set59      |NA    |1     |2         |       78|       63|
## |set59      |NA    |1     |3         |       83|       35|
## |set59      |NA    |1     |4         |      116|       19|
## |set59      |NA    |1     |5         |      122|       24|
## |set59      |NA    |1     |6         |      166|       29|
## |set59      |NA    |1     |7         |      157|       28|
## |set59      |NA    |1     |8         |      175|       44|
## |set59      |NA    |1     |9         |      170|       36|
## |set59      |NA    |1     |10        |      183|       30|
## |set59      |NA    |1     |11        |      182|       30|
## |set59      |NA    |1     |12        |      126|       23|
## 
## 
## |Experiment | sum_live| sum_dead|
## |:----------|--------:|--------:|
## |Set26      |    49800|     2196|
## |Set29      |    22466|      977|
## |Set30      |     5587|      508|
## |Set32      |     3502|      561|
## |Set33      |     9435|      363|
## |Set34      |     3961|      187|
## |Set35      |    11351|      417|
## |Set36      |    34335|      909|
## |Set40      |    70698|    10421|
## |Set44      |     9489|     2189|
## |Set45      |    53587|     2610|
## |Set51      |    15814|     2102|
## |Set52      |     3248|     3244|
## |set57      |    13691|     3389|
## |set58      |     8444|      339|
## |set59      |     4797|      940|

————————————————————————

Odds Ratio Comparing Class:

Odds Ratio Comparing: 0 vs 1 with no drug

[1] “Overall significance (p-value) of association across all time-points = 5.62717640786736e-19”

[1] “Akaike Information Criterion (AIC) = 19105.1964597778”

glm - 0 vs 1
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.1872307 0.3178228 -10.028326 0.0000000
Class1 0.7465097 0.2727943 2.736530 0.0062091
Timepoint 0.0945551 0.0035590 26.568141 0.0000000
Class1:Timepoint -0.0455014 0.0050324 -9.041757 0.0000000
OR Time lower upper lower99 upper99 pvalue Reference Compare
2.109624 0 1.2359414 3.600910 1.0450497 4.258662 0.0062091 0 1
2.015784 1 1.1819349 3.437910 0.9996421 4.064841 0.0100622 0 1
1.926119 2 1.1300835 3.282884 0.9559799 3.880765 0.0159735 0 1
1.840442 3 1.0803103 3.135419 0.9140063 3.705910 0.0248199 0 1
1.758576 4 1.0325410 2.995124 0.8736663 3.539782 0.0377211 0 1
1.680351 5 0.9867038 2.861629 0.8349063 3.381912 0.0560404 0 1
1.605606 6 0.9427292 2.734583 0.7976745 3.231859 0.0813486 0 1
1.534186 7 0.9005498 2.613655 0.7619201 3.089205 0.1153435 0 1
1.465943 8 0.8601009 2.498531 0.7275940 2.953554 0.1597174 0 1
1.400735 9 0.8213193 2.388912 0.6946484 2.824536 0.2159802 0 1
1.338428 10 0.7841442 2.284516 0.6630366 2.701796 0.2852532 0 1
1.278892 11 0.7485167 2.185076 0.6327135 2.585003 0.3680621 0 1
OR Time lower upper lower99 upper99
1.66289 5.5 0.9754063 2.834929 0.8250698 3.351485

First half Mean

OR Time lower upper lower99 upper99
1.888483 2.5 1.107919 3.218979 0.9372084 3.805312

Second half Mean

OR Time lower upper lower99 upper99
1.437299 8.5 0.8428933 2.450879 0.7129312 2.897659

Odds Ratio Comparing: 1 vs 0 with no drug

[1] “Overall significance (p-value) of association across all time-points = 5.6271763278236e-19”

[1] “Akaike Information Criterion (AIC) = 19105.1964597493”

glm - 1 vs 0
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.4407361 0.3160926 -7.721585 0.0000000
Class0 -0.7464977 0.2728465 -2.735962 0.0062198
Timepoint 0.0490534 0.0035623 13.769981 0.0000000
Class0:Timepoint 0.0455014 0.0050324 9.041740 0.0000000
OR Time lower upper lower99 upper99 pvalue Reference Compare
0.4740238 0 0.2776825 0.8091924 0.2347868 0.9570324 0.0062198 1 0
0.4960908 1 0.2908481 0.8461669 0.2459820 1.0005044 0.0100778 1 0
0.5191850 2 0.3045828 0.8849913 0.2576497 1.0461999 0.0159956 1 0
0.5433543 3 0.3189080 0.9257653 0.2698063 1.0942439 0.0248503 1 0
0.5686488 4 0.3338461 0.9685945 0.2824689 1.1447683 0.0377617 1 0
0.5951208 5 0.3494201 1.0135902 0.2956548 1.1979129 0.0560928 1 0
0.6228251 6 0.3656538 1.0608699 0.3093820 1.2538256 0.0814141 1 0
0.6518191 7 0.3825719 1.1105577 0.3236689 1.3126629 0.1154223 1 0
0.6821629 8 0.4001997 1.1627848 0.3385344 1.3745904 0.1598089 1 0
0.7139192 9 0.4185637 1.2176894 0.3539981 1.4397834 0.2160822 1 0
0.7471539 10 0.4376911 1.2754176 0.3700801 1.5084273 0.2853623 1 0
0.7819357 11 0.4576099 1.3361236 0.3868009 1.5807185 0.3681735 1 0
OR Time lower upper lower99 upper99
0.6163533 5.5 0.3614648 1.050979 0.3057344 1.242556

First half Mean

OR Time lower upper lower99 upper99
0.5327373 2.5 0.3125479 0.9080501 0.2643914 1.073444

Second half Mean

OR Time lower upper lower99 upper99
0.6999693 8.5 0.4103817 1.193907 0.3470774 1.411668

[1] TRUE TRUE

Odds Ratio Combined

Reference condition: 0

Odds Ratio Combined

Reference condition: 1

] NULL

[[2]] NULL